Reports of “cyclospora,” the microscopic parasite infecting people in several states, have been multiplying. The epicenter of the diarrheal pathogen outbreak is currently in Michigan, with several other Midwest and mid-Atlantic states affected. Though the source remains unclear, lettuce and/or salad greens appear to be the leading culprit as of now, subject to confirmation from other states.

Cases of cyclospora have been mounting since late spring. So what’s taken so long to get this information? Why don’t we already know what product (or products) are making people sick? And why has the Centers for Disease Control and Prevention been so quiet?

The answers are complicated and a bit messy, due to characteristics of both the pathogen and the public health response.

First, federal case counts have lagged numbers reported by individual states. As of July 13, there were 1,645 cases of cyclosporiasis reported to the CDC, originating in 34 states. Astute readers will spot that number is very different from the 3,762 cases reported in Michigan alone as of July 15. This discrepancy is largely due to disconnect and delayed reporting and confirmation of cases between states and the CDC.

The CDC notes some of these cases “require further analysis to confirm the illness as domestically acquired cyclosporiasis.” Further, cases acquired months ago are less likely to be part of the current outbreak, so the national numbers alone are misleading when discussing ongoing transmission. There are concerns that the Trump administration’s removal of cyclospora from the FoodNet surveillance system and the dissolution of the Division of Parasitic Diseases and Malaria may have slowed detection and response.

Second, cyclospora has a fairly lengthy incubation period. The time from exposure to the parasite to the development of the watery diarrhea symptoms can be as long as two weeks. That makes trackback work — figuring out everything a case patient ate during that incubation period — a difficult task. (Could you detail everything you ate in the past two weeks, including condiments?)

Third, because cyclospora is a protozoan (single-celled) parasite, the laboratory work is more challenging than for your basic virus or bacterium. You can’t just grow it in a petri dish or in cell culture as is done for most bacteria or viruses. Instead, the stool sample may need to be concentrated and stained for oocysts (thick-walled spores). But there are problems. There might not be enough oocysts in a particular sample for identification, for example, so multiple samples may be needed.

Further, while some labs may have tests that can detect the parasite in as little as an hour, “others rely on reference laboratory PCR [polymerase chain reaction] testing or traditional ova-and-parasite examinations,” explained Rodney E. Rohde, chair and professor in the Medical Laboratory Science Program at Texas State University. “Not all gastrointestinal panels include cyclospora, and not every laboratory routinely performs testing for intestinal parasites,” Rohde said.

This all makes diagnosis a, um, crapshoot.

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But let’s take a step back: Often, a physician first must suspect cyclospora infection and then order the specific test to detect the pathogen in the stool. As it’s not on every routine diarrhea testing panel, cases may have already been missed.

And finding the parasite is just the beginning. What’s missing so far in this outbreak is confirmation that these cases are all even related — that they have a common source, such as the maybe-implicated lettuce or other items like berries. This is done in two ways: by the trackback work, looking for commonality in what and where people ate, and by molecular analyses, showing the pathogens from these different states and cities are identical at the molecular level (or very close to it).

Like detection, this molecular detective work is more difficult with a parasite. Cyclospora’s genome size is about 10 times that of E. coli or salmonella, and about 6,000 times larger than norovirus, a common diarrheal virus. Because of this and the inability to grow the parasite directly in the lab, direct DNA sequencing isn’t used, but instead a molecular genotyping method “that analyze(s) multiple genetic markers across the parasite’s genome to determine how closely isolates are related,” per Rohde.

But Rohde notes this analysis is limited to specialized public health and reference laboratories and coordinated by the CDC, so your ordinary hospital laboratory would not be able to generate that information.

When acquired, these molecular data can be used like a crime scene fingerprint: If you see a matching pattern in samples from people’s stool and from the tested food products or farms where products originated, that serves as the closest thing we have to a smoking gun showing the outbreak’s origin.

Such a challenging epidemic requires strong federal leadership, both for rapid response to the outbreak and for timely information so that consumers are educated and can protect themselves. So far, we’ve seen little of that.

It’s not clear why the CDC excluded other states with high case counts, including New York and Illinois, when so much data are missing.

While the CDC was presumably coordinating this multistate outbreak response behind the scenes, the organization was absent from discussion of the epidemic until July 15, when it posted several pages on overall surveillance for cyclospora and a second notice that the outbreak may be limited to four states: Michigan, Ohio, West Virginia and Kentucky. It’s not clear why the CDC excluded other states with high case counts, including New York and Illinois, when so much data are missing. The affected areas may expand as more case data are analyzed. Perhaps having a confirmed director of the organization would help right the ship.

As for changes made to FoodNet surveillance, Rohde said it would be difficult to claim these changes directly caused delay but noted that “reducing active surveillance can limit our ability to detect changes in disease burden, recognize emerging trends early and evaluate the effectiveness of prevention strategies over time.” The removal may not have hindered current efforts but may hobble us in the future.

The cyclospora outbreak is exposing some of the limitations of our current system, which Rohde equates to assembling a jigsaw puzzle. If one piece is missing or delayed, the entire investigation takes longer. As a person in one of the affected states, I’m avoiding bagged leafy greens and using the cherries I recently purchased for baking instead of snacking raw, just in case.

Tara C. Smith

Tara C. Smith is a professor of epidemiology at Kent State University’s School of Public Health. Before that, she spent nine years in the Department of Epidemiology at the University of Iowa College of Public Health, where she directed the college’s Center for Emerging Infectious Diseases.